The MainConcept h.264 encoder for Premiere Pro CS5.5 is simply aweful, but I imagine I don't need to tell anyone that.

Way-back-when when I did AMVs, I'd typically export Lagarith Lossless out of Premiere and load it into something else to encode but I was out of AMVs (And editing in general) for some years and I never found an external h.264 encoder I liked.

I did become fond of Handbrake for ripping DVDs to h.264 for my HTPC, but it can't seem to open Lagarith files nor the Debugmode FrameServer's AVI Signpost.

So simply put, what workflow should I be using to get GOOD h.264 out of Premiere to maximize the quality of works that are due for YouTube and other methods of distrobution?

My workflow is Edit -> export lagarith -> encode with command-line x264 -> Mux (generally mkv: h.264+FLAC). Encoding with x264 is actually pretty easy to learn, and will most likely give you the results you want. As far as YouTube goes, I'm still trying to figure that out.

Do what Cannonaire said (maybe use utvideo so you get commandline x264 working if you're a mac user). Main reason you had issues with Handbrake is that it sucks. There are no good encoders other than x264 so you really need a decent build of that against a recent libav, JEEB's builds are great and can be thrown into ZarxGUI if it doesn't already use them.